Hand folding de novo S pletsch
21:55:25 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375732527.png 21:56:26 pick an end and band sidechains with 3 or less segments between them 21:56:32 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375732594.png 21:57:12 since the turn is short, it can be assuemd these go together 21:57:14 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375732636.png 21:57:33 here too 21:57:36 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375732658.png 21:57:58 and here 21:58:01 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375732683.png 21:58:21 so end up with 3 sheet groups 21:58:23 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375732705.png 21:58:55 couple bands to hold together 21:58:58 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375732740.png 21:59:15 a couple to pull it together 21:59:17 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375732759.png 21:59:34 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375732775.png 22:00:07 now is where i would normally look at server prediction on puzzle page 22:00:54 there is enough chance that the 3 helix segments are one helix (since it's not likeley there at all anyway, to join them into one 22:01:04 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375732865.png 22:01:54 rebuild into helix shape 22:02:12 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375732933.png 22:02:47 freeze structures 22:02:51 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375732973.png 22:03:45 start with first sheet group 22:03:53 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375733035.png 22:04:08 going to shift middle sheet to put phobics on same side as other sheet 22:04:19 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375733060.png 22:04:38 band 22:04:41 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375733082.png 22:05:18 wiggle them together 22:05:31 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375733133.png 22:05:46 i think that right one will come down a couple segments, but we will see 22:06:18 band next set and wiggle together 22:06:22 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375733184.png 22:06:55 helix in the way so band it out and rebuild to move 22:06:58 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375733220.png 22:07:04 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375733226.png 22:07:27 tweak shift sheet 22:07:34 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375733256.png 22:07:54 reband 22:08:04 and wiggle 22:08:07 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375733289.png 22:09:18 won't pull together so rebuild turn 22:09:21 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375733363.png 22:09:50 STILL WON'T PULL TOGETHER SO SHORTEN SHEET 22:09:59 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375733401.png 22:10:41 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375733443.png 22:11:04 join 2 short sheets 22:11:07 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375733469.png 22:12:46 bandies 22:12:48 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375733570.png 22:13:42 sometimes you have to move the larger sidechains to get the sheets to pull together or the sidechains will push them away from each other, or make only part connect 22:15:30 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375733731.png 22:15:38 had to kill the two single helix dots at the ends of the sheets to get them to connect too 22:16:09 now shake and wiggle out 22:18:13 dosome inor rebuilds to clean up turns between sheets to free up where they are binding and not connecting with h bonds 22:18:24 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375733905.png 22:19:21 and it's still rough but coming together 22:19:36 shake and wiggle out to get sheets to settle in together 22:19:42 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375733983.png 22:20:41 now to try and figure out hwo the three sets of sheets come together and where to stick the helix 22:21:10 The place where I usually get stuck. 22:21:21 a lot of large sidechains on this one, tryptophan, tyrosine, and phenalalanine 22:21:50 those often group together and stack on top of each other, not so much trpy but the other two 22:22:40 so i'm going to take a stab at it that they gome somewhere in these areas and band 22:22:45 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375734168.png 22:23:29 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375734211.png 22:23:34 do you change options on those rubber bands? or just go with the default? 22:23:40 default 22:24:00 can weaken thme if you want, but i usually just wiggle in short bursts to keep it all together 22:24:24 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375734265.png 22:24:33 one set is trying to pull to the side of the other 22:25:06 i'l take that as a sign from the folding gods 22:25:09 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375734311.png 22:25:51 you just became my handfold god 22:25:57 lol 22:26:01 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375734363.png 22:26:03 heh 22:26:07 other one wants in the act too 22:26:13 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375734375.png 22:26:56 it's ugly with mismatched sheets 22:27:02 different lengths and all together 22:27:26 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375734447.png 22:27:50 bring helix in 22:27:53 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375734475.png 22:29:29 and now try to figure out a way to make it look liek a real protein 22:29:36 unfreeze 22:29:40 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375734581.png 22:29:44 shake wiggle 22:30:21 sometimes I wish I could physically take them in my hands and shape them... 22:30:34 maybe one day haptics will be good enough... 22:30:38 there are ways 22:30:40 lol 22:31:25 after its settled together ok, kill bands 22:31:29 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375734690.png 22:31:41 wiggle it out 22:32:16 still far from right, but it's a starting point that has some structure to work with 22:32:19 IMAGE: http://fold.it/portal/files/chatimg/irc_40708_1375734741.png 22:32:38 ;) fin ! I think 22:32:49 now comes the hard part of trying different configurations 22:33:32 i will usually rebuild out the reddest spots first though to get rid of kinks and have an idea of where different sheet placements will score 22:40:05 <@marie_s> for precision , al was ci=1? 22:40:12 YEAH 22:40:22 I DON'T BOTHER WITH CI TILL LATER USUALLY 22:40:27 stupid cpas key 22:40:46 beset by typo demons 22:41:11 i think i dropped it to about .15 once to shake when a lot of stuff was bunched together Hand fold step 1.png Hand fold step 2.png Hand fold step 3.png Irc 40708 1375732636 step 4.png Irc 40708 1375732658.png Irc 40708 1375732683.png Irc 40708 1375732705.png Irc 40708 1375732759.png Irc 40708 1375732775.png Irc 40708 1375732865.png Irc 40708 1375732933.png Irc 40708 1375732973.png Irc 40708 1375733035.png Irc 40708 1375733060.png Irc 40708 1375733133.png Irc 40708 1375733184.png Irc 40708 1375733220.png Irc 40708 1375733226.png Irc 40708 1375733256.png Irc 40708 1375733289.png Irc 40708 1375733363.png Irc 40708 1375733401.png Irc 40708 1375733443.png Irc 40708 1375733469.png Irc 40708 1375733570.png Irc 40708 1375733731.png Irc 40708 1375733905.png Irc 40708 1375733983.png Irc 40708 1375734168.png Irc 40708 1375734211.png Irc 40708 1375734265.png Irc 40708 1375734311.png Irc 40708 1375734363.png Irc 40708 1375734375.png Irc 40708 1375734447.png Irc 40708 1375734475.png Irc 40708 1375734581.png Irc 40708 1375734690.png Irc 40708 1375734741.png Category:Strategy